Collaborations

Genedata and the Center of Information Sciences and Databases (C-ISD) collaborated on establishing an integrated solution for the management and analysis of data from High Content Screening measurements with a focus on the needs of large-scale screening efforts in private and public research.

"openBIS for High Content Screening (HCS)" provides an open, distributed system for managing HCS image data and related sample information. It supports a variety of HCS measurement instruments and is able to manage, visualize and query for metadata, raw and result data on the level of the screening library, experiment and sample annotation, images, well- and plate-based features and feature-selection results. It was developed by C-ISD together with partners from both, academia and industry. Important partners have been the RTD projects InfectX and LipidX in the context of SyBIT support projects.

The Sanofi Oncology Target Discovery group has established a novel and agile automated platform for functional genomic and compound screening. To effectively and efficiently use data generated by such a comprehensive robotics system, the Target Discovery group identified the need for a unified data management platform (the ‘TIDVal platform’) to: 1) cover a broad range of screening applications and technologies in a single environment; 2) enable the efficient comparison of experimental conditions and results across multiple cell lines; 3) support multiple substances (combinations from small molecules and biological substances) per well in the same plate (an industry first); and 4) have the solution built in parallel to the setup of the lab automation and biological research.
In a collaboration of Sanofi, Genedata and the Center for Information Sciences and Databases (C-ISD), the TIDVal system has been designed and built. C-ISD has contributed "openBIS for HCS", which provides an open, distributed system for managing HCS image data and related sample information. It supports a variety of HCS measurement instruments and is able to manage, visualize and query for metadata, raw and result data on the level of

the screening library,

experiment and sample annotation,

images,

well- and plate-based features,

feature-selection results.

It allows cross-domain queries of these and other data and metadata tyes and provides intuitive visualization for them. In the TIDVal Project, data from the diverse sources described above were collected and managed, browsed, annotated, visualized and made available to the project’s data analysis system "Genedata Screener for HCS".

There is currently no public information on the Sanofi TIDVal system.

Inspired by patients and the limitations of conventional approaches to cancer treatment, Agios is forging a new and different path to treating cancer and rare genetic disorders known as inborn errors of metabolism (IEMs) by targeting dysfunctional cellular metabolism.

Agios has a robust platform to interrogate the differential cellular metabolism of diseased cells relative to normal cells. An integral part of this platform is the database system "openBIS for High Throughput Metabolomics", which was developed by the Center for Information Sciences and Databases (C-ISD) together with the Zamboni and Sauer labs of ETH Zurich as part of a SyBIT effort to support the RTD project YeastX and in a joint project with Agios adapted to its metabolomics platform.

Sophia Genetics offers solutions for the secure storage and analysis of patient genome sequence information to enable its effective, confidential application to personalized healthcare. Sophia Genetics and the EPFL Bioinformatics and Biostatistics Core Facility are collaborating on developing processing and visualization tools for genetic variants in the context of specific biological and medical questions.

We focus on scaling to genome-wide, high-coverage data and interpretation of multi-gene contexts.

The Scientific Gateway-Based User Support SCI-BUS Project is an EU FP7 project that focuses on easy to use science gateways. SyBIT provides the use-case for the proteomics gateway developed at the ETH Zurich. The gateway will be rendered into a public service by SCI-BUS and SyBIT (see also iPortal).

KNIME (Konstanz Information Miner) is a user-friendly and comprehensive open-source data integration, processing, analysis, and exploration platform. From day one, KNIME has been developed using rigorous software engineering practices and is used by professionals in both industry and academia in over 60 countries.

KNIME grows to accommodate your demand for data analytics.
While KNIME Team Space suits small teams, the KNIME Server provides support for a full corporate setting including user authentication, remote execution, scheduling, SOA integration and a configurable web browser user interface. When combined with KNIME Cluster Execution the workflows can be sent to a compute cluster for parallel execution.

Genohm provides a Laboratory Information Management System (LIMS) combined with an Electronic Lab Notebook (ELN) that is especially well suited to biology research labs in academia. SyBIT supports the Genohm SLIMS system, which has been acquired by several SystemsX.ch labs all over the country.

SLIMS has been engineered with configurability and flexibility in mind, which is necessary to be able to adapt it to the very heterogeneous needs of academic research labs.

The SiLA consortium for Standardisation in Lab Automation, develops and introduces new device and data interface standards allowing rapid integration of lab automation and data management systems. Leading system manufacturers, software suppliers, system integrators and pharma/biotec corpo­ra­tions form the SiLA consortium and contribute in different technical work groups with their highly skilled experts.

SiLA is a not-for-profit membership corporation with global footprint. Membership is open for institutions, corpo­ra­tions and individuals active in the life science lab auto- mation industry.
The SiLA consortium provides professional training, support and certification services to suppliers and system integrators implementing SiLA compliant interfaces.

The Center for Information Sciences and Databases (C-ISD) is running a software project with a Top10 pharmaceutical company in the field of High Througput Sequencing data management. The projects are based on openBIS technology and software modules have been developed simultaniously together with SystemsX.ch RTD projects on the SyBIT mandate and with the industry partners. This has been a win-win situation for both sides, the RTD projects and the companies, as synergies could be leveraged and a sustainable environment for the software created in these projects could be established.